Four Corners reports Murray-Darling Basin Plan rorts in NSW | VIDEO

Outrage is being felt across the Murray-Darling Basin after allegations of water theft and collusion between irrigation lobbyists and the New South Wales government.

On Monday night, the ABC TV show Four Corners reported that water bought by taxpayers for environmental purposes was being used to irrigate cotton farms in the Barwon-Darling river system.

Water meters were being tampered with, a NSW government official offered to pass confidential documents to lobbyists, and NSW sought legal advice about whether to withdraw from the Murray-Darling Basin Plan, the national agreement on water use, the program alleged.

Demands for an independent enquiry have since flowed thick and fast from politicians, environmental groups and residents of river towns.

South Australian Water Minister Ian Hunter said the Four Corners report had confirmed his "deep suspicions" about the level of commitment to the basin plan in NSW.

He hoped the cheating of the basin plan was confined to a "rogue element" of cotton and rice growers along the Barwon River, but was concerned that the NSW public service appeared to have condoned it.

"What senior bureaucrat doesn't report that to the minister's office?" he asked.

"Those ministers, when were they informed, how much did they know and what did they do?

"We need to find out how far it goes."

He suggested responsibility for basin plan compliance and enforcement be taken away from state authorities and given to the Murray-Darling Basin Authority (MDBA) or another federal agency.

If NSW could not fulfil its basin plan commitments, he said, the federal government should step in and buy back water to make up any shortfall.

"This plan was designed to ensure the River Murray could sustain a drought," he said.

"If the river is compromised again by a serious drought and we haven't put these changes in place, the river will die and the towns which rely on the river will wither.

"It's not in New South Wales' interests to withdraw from the plan, not in its towns' or its citizens' interests."

The basin plan's architect, federal Labor MP Tony Burke, said the revelations proved Nationals MP Barnaby Joyce should never have been made the federal minister for both water and agriculture.

But state Australian Conservatives MP Robert Brokenshire said Mr Joyce should be put in charge of the investigation.

"We have suspected for some time ... that there has not been proper control and investment from the Murray-Darling Basin Authority," he said.

Senator Nick Xenophon called for a judicial inquiry and described the allegations as an "attack on what federation stands for".

Greens Senator Sarah Hanson-Young, who wanted a Senate enquiry, said taxpayers' money was being used to line the pockets of big irrigators.

"River communities have every right to feel betrayed," Senator Hanson-Young said.

Conservation Council SA chief executive Craig Wilkins said it was now crunch time for the basin plan.

"The next six months will determine whether the Murray system will be given a decent shot at survival or whether we are witnessing hyper-expensive window dressing on a fundamentally unsustainable irrigation industry," he said.

"The sight of mega dams bulging with water to service a tiny number of rich irrigators while downstream the river withers is deeply distressing.

"It's essential an urgent public inquiry is held to restore the public's trust in this vital nation-building program."